Detection and genetic characterization of Seoul Virus and other viruses borne by commensal Norway rats (Rattus norvegicus) in France Michel Pépin University of Lyon, VETAGROSUP, Lyon, FRANCE

Norway rat (Rattus norvegicus) : an invasive species Virology

Norway rat (Rattus norvegicus) : an invasive species = a pest Commensal rodent species Responsible for damage/waste to agriculture, forestry, horticulture and infrastructures  huge financial losses  global demand for food  Damage level is likely to increase Anticoagulant rodenticides ✚✚✚ … BUT anticoagulant-resistant rats exist now Virology

Norway rat (Rattus norvegicus) : reservoir of pathogens VIRUSES Seoul virus (SEOV; Bunyaviridae; hantavirus) ; cowpox virus (CPXV; Poxviridae) ; hepatitis E virus (HEV; orthohepevirus, Hepeviridae); lymphocytic choriomeningitis virus (LCMV; Arenaviridae); encephalomyocarditis virus (EMCV; Picornaviridae) BACTERIA Leptospira interrogans ; Streptococcus moniliformis ; Pasteurella sp ; Yersinia sp ; Francisella tularensis ; Erysipelothrix rhusiopathiae ; Bartonella sp; antibiotic-resistant bacteria PARASITES & FUNGI Trichinella sp ; Toxoplasma gondii ; Hyminelopis sp ; dermatophytes Virology

Rat = silent carrier & professional excretor  survey of brown rats in and around Lyon (France) Virology

Three populations of rats ➜ 178 rats trapped in and around Lyon (EU « Wildtech » survey : Drs F Ayral and M Artois ; Epidemiol. Infect, 2014) ➜ 16 rats trapped in the « Parc de la Tête d’Or » (« PERS PTO » survey : Drs T Dupinay, M-H Laaberki, M Attoumane & M Pépin) ➜ 28 wild rats trapped and maintained in captivity (« PERS VAS » survey) SurveyAdultsMaleFemaleTotal WildTech63%96 82 * 178 PERS PTO ** 50%9716 PERS VAS100%028 * 18 pregnant femal ** Mean weight = 268 g (373 g-176 g) Mean length ( without tail ) = 24.1 cm (27 cm – 22 cm) Virology PERS = Pathogènes Emergents et Rongeurs Sauvages (or Emergent Pathogens and Wild Rodents) PTO = Parc de la Tête d’Or VAS = VetAgroSup

« Wildtech » population Pathogen Leptospira interrogans (n= 171) SEOV (n= 128) HEV (n= 142) Toxoplasma gondii (n= 77) % of positive animals 26%14% 8% Assayrt-PCRRT-PCR Serology SampleKidneyLung Liver & feces Blood Adapted from F Ayral et al, Epidemiol Infect, 2014 Doi: /S ) Virology

« PERS » populations  pathogens identified Leptospira interrogans (about 60% of positive rats in PERS PTO population) (A-L Zilber, personal communication) Seoul virus (SEOV) ?? r-Hepatitis E virus (r-HEV or HEV-C1 # ) : 18% positive rats in PERS VAS; no positive in PERS PTO population* RMV-1** (rat minute virus = parvovirus) : 69% in PERS PTO ; 7% in PERS VAS #Smith et al (2014), J Gen Virol,95, *Results confirmed by Dr Rainer Ulrich, FLI, Germany ** not zoonotic Virology

Hantaviruses and SEOUL VIRUS (SEOV) Hantaviruses belong to the Bunyaviridae family of viruses 24 hantavirus species in current ICTV (2013 release) Negative strand Enveloped RNA viruses Tri-segmented genome : L, M & S Reservoir hosts : rodents, shrews, moles and bats HFRS & HPS = hantavirus disease HTNV & SEOV, PUUV & DOBV, SNV & ANDV Virology Figure from A Vaheri, Nature Reviews Microbiology 2013

Infected rodent : silent carrier & professional excretor Virions in excreta (urine, feces, saliva) Biting, fighting, sexual behavior Naive rodent Virions in excreta (urine, feces, saliva) Cycle of transmission of SEOV Virology

Optimization of sample preparation  NGS qPCR : HTNV/GAPDH/  -actin G RINDING N UCLEASE TREATMENT FOR HOST GENOME DEGRADATION V IRAL RNA E XTRACTION & Q PCR C LARIFICATION DNA RNA C ELLULAR LYSIS : F REEZE - THAW (3 X ) Viral RNA Virology

Optimization of NGS (Illumina® & 454®) for complete genome SEOV detection Viral reads were 6 times more abundant in the S3 sample (2.20%) in comparison to the S1 sample (0.34%) Complete SEOV genome recovery Extraction Filtration 0,45 µm membrane PES 1 Nuclease 90 min Lung LYO852 Homogenization Freeze-Thaw 3X Centrifugation 23 Ribosomal depletion Library amplification Sequencing Sample Read data % rat host% Ribosomal% viral reads % of SEOV reads 188,16%0,99%0,34%20 % 271,78%30,95%0,73%21 % 347,66%21,55%2,20%84 % Virology

LYO852 strain genome appears to belong to the lineage 7 of SEOV Shows a very high identity to European strains And is very similar to 2012 Human Lyon SEOV Phylogenetic analysis of the complete SEOV sequence Virology

Virology

Virome of 10 rats (PERS PTO population) M &M : Illumina HiSeq rats Sample = lungs Viral enrichment = 3.46% (range : 1.46 – 5.21) Sequences of phages and endogenous retroviruses Negative for hantaviruses (SEOV) & HEV = confirmation of PCR results 2 unexpected viruses (>10 aligned reads & >10% of genome covered) : 1. Semliki forest virus (SFV) : alphavirus & arbovirus 2. Nyamanini virus (NYMV) : nyavirus (order Mononegavirales, family of Nyamiviridae) = a tick-borne virus Virology

Conclusions 1. Optimisation of sample preparation  full length viral sequences from tissue samples with very low amounts of viral RNA  rodent-borne pathogens (known and unknown) 2. Confirmation of the relative high prevalence of SEOV in rats both in rural and urban environments  human cases First full sequence of SEOV in France Despite global distribution, most SEOV are genetically homogenous : >95% nt sequence identity 3. Analysis of virome by NGS : 2 unexpected viruses (SFV & NYMV)  these results need confirmation !! Virology

Collaborations 1. « Wildtech » programme and PERS group, VetagroSup, Veterinary Faculty, Lyon (Fr) = Drs F Ayral & M Artois 2. ANSES-Lyon (Fr) : Dr P Marianneau 3. ProfileXpert, University of Lyon (Fr) : Drs C Legras-Lachuer & J Lachuer 4. AHVLA, Addlestone (UK) = Drs L McElhinney, KC Pounder, DA Marston & A Fooks 5. PERS group, VetagroSup, Lyon (Fr) : Drs T Dupinay, M-H Laaberki & M Pépin ; student : M Attoumane Virology

And the winner is ? Virology